The normal place for specifying the target machine is just what you changed: Linker -> Advanced -> Target Machine. But OpenCV comes with a little extra gotcha. In Linker -> All Options -> Additional Options, it specifies /machine:X86. When you create a new x64 Platform target from the Win32 Platform, that little bit of configuration comes along for the ride.
So, for your x64 targets, go into Linker -> All Options -> Additional Options and remove /machine:X86. Then, the configuration will come from Linker -> Advanced -> Target Machine, just as you'd expect.